Judge Bill Woody said the Dallas County medical examiner made the provisional identification based on circumstances of the case as described by investigators. DNA test results are pending, and X-ray tests will be conducted to determine if the boy was starved to death, he added.

The medical examiner's office declined to comment because the case involves remains found in another county.

The boy's father, Aaron Ramsey, and his stepmother, Elizabeth Ramsey, face charges of injury to a child. Each is being held at the Dallas County Jail on $500,000 bail.

Authorities say the boy was confined to a room and starved as punishment.

According to affidavits, the boy's father said he found the boy unconscious in his room and that he wrapped the child up and put him in a vacant nearby house's storm shelter. Ramsey told investigators he dumped the boy's body in Ennis, Texas, a day or two later.

The Dallas Morning News reported that the remains were discovered Saturday in a creek bed where authorities say the child's father told police he put the body last year. The bones also were inside a sleeping bag matching one described by the father.

The remains were found "under a log" in three feet of water, Woody said.

Starla Swanson, the boy's maternal step-grandmother, said the medical examiner's office contacted Johnathan's mother with the news on Wednesday.

"It's been very rough knowing that he's been gone this long," Swanson said. "Her emotions and the whole family's are so mixed, but now it's become painfully real."

The Associated Press and msnbc.com's Alastair Jamieson contributed to this report.